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UG integration tests updated. A handful of sites are lost because there are only 5 indels and one starts at the beginning of the read so it no longer passes our min threshold (now consistent with GGA), but mostly the depth changes ever so slightly once in a while between extended and normal pileups (I think the normal pileups are correct). I have looked thoroughly in IGV at ALL differences and am happy with the new results. As an aside, the AD is now calculated more accurately for indels.

This commit is contained in:
Eric Banks 2012-03-30 01:35:49 -04:00
parent f4d4969f23
commit 16bef191c6
1 changed files with 19 additions and 19 deletions
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38
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -30,7 +30,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("ac3737b4212f634a03c640c83f670955"));
Arrays.asList("d3191b2f10139c969501990ffdf29082"));
executeTest("test MultiSample Pilot1", spec);
}
@ -54,7 +54,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList("c5b53231f4f6d9524bc4ec8115f44f5c"));
Arrays.asList("7c7288170c6aadae555a44e79ca5bf19"));
executeTest("test SingleSample Pilot2", spec);
}
@ -62,7 +62,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + validationDataLocation + "multiallelic.snps.bam -o %s -L " + validationDataLocation + "multiallelic.snps.intervals", 1,
Arrays.asList("6f70dfbaf3bb70c702f9e9dbacd67c17"));
Arrays.asList("c956f0ea0e5f002288a09f4bc4af1319"));
executeTest("test Multiple SNP alleles", spec);
}
@ -72,7 +72,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "a08df9aea2b3df09cf90ff8e6e3be3ea";
private final static String COMPRESSED_OUTPUT_MD5 = "2158eb918abb95225ea5372fcd9c9236";
@Test
public void testCompressedOutput() {
@ -93,7 +93,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
String md5 = "6358934c1c26345013a38261b8c45aa4";
String md5 = "834e85f6af4ad4a143b913dfc7defb08";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@ -147,7 +147,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-sites_only", "44f3b5b40e6ad44486cddfdb7e0bfcd8" );
e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "ecf92054c1e4bd9d6529b8002d385165" );
e.put( "--output_mode EMIT_ALL_SITES", "119c9fcefbc69e0fc10b1dc52f6438e3" );
e.put( "--output_mode EMIT_ALL_SITES", "e10819a2a7960254e27ed2b958b45d56" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -181,8 +181,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 0.01, "926b58038dd4989bf7eda697a847eea9" );
e.put( 1.0 / 1850, "93f44105b43b65730a3b821e27b0fa16" );
e.put( 0.01, "d5879f1c277035060434d79a441b31ca" );
e.put( 1.0 / 1850, "13f80245bab2321b92d27eebd5c2fc33" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -206,7 +206,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("a1b75a7e12b160b0be823228c958573f"));
Arrays.asList("8c134a6e0abcc70d2ed3216d5f8e0100"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -225,7 +225,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("3bda1279cd6dcb47885f3e19466f11b9"));
Arrays.asList("34baad3177712f6cd0b476f4c578e08f"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -244,7 +244,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("d9fc3ba94a0d46029778c7b457e7292a"));
Arrays.asList("4bf4f819a39a73707cae60fe30478742"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -259,7 +259,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("b2e30ae3e5ffa6108f9f6178b1d2e679"));
Arrays.asList("ae08fbd6b0618cf3ac1be763ed7b41ca"));
executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
}
@ -272,7 +272,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("2cd182a84613fa91a6020466d2d327e2"));
Arrays.asList("120600f2bfa3a47bd93b50f768f98d5b"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -282,7 +282,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("9cd08dc412a007933381e9c76c073899"));
Arrays.asList("2e75d2766235eab23091a67ea2947d13"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -292,7 +292,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("5ef1f007d3ef77c1b8f31e5e036eff53"));
Arrays.asList("5057bd7d07111e8b1085064782eb6c80"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
}
@ -300,13 +300,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSampleIndels() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("fbc48d7d9e622c9af7922f91bc858151"));
Arrays.asList("c0f9ca3ceab90ebd38cc0eec9441d71f"));
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
Arrays.asList("94c52ef70e44709ccd947d32e9c27da9"));
Arrays.asList("0240f34e71f137518be233c9890a5349"));
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
}
@ -349,7 +349,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction0() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
Arrays.asList("f08ff07ad49d388198c1887baad05977"));
Arrays.asList("53758e66e3a3188bd9c78d2329d41962"));
executeTest("test minIndelFraction 0.0", spec);
}
@ -357,7 +357,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMinIndelFraction25() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
Arrays.asList("a0945fd21369aaf68c7f1d96dbb930d1"));
Arrays.asList("3aa39b1f6f3b1eb051765f9c21f6f461"));
executeTest("test minIndelFraction 0.25", spec);
}